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2cqm

Solution structure of the mitochondrial ribosomal protein L17 isolog

Method: SOLUTION NMR Dmax: 65.2 Å Quality: REASONABLE
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Ribosomal protein L17 isolog

Homo sapiens

UniProt Q9NRX2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 28–136 Fragment：Mitochondrial ribosomal protein L17 No other associated polymer SOLUTION NMR NMR measurement conditions：pH 7；298 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition：1.1mM 13C/15N-PROTEIN; 20mM d-Tris-HCl; 200mM NaCl; 1mM d-DTT; 0.02% NaN3 | 90% H2O/10% D2O Resolution not provided

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 2CQM Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3IY9 Leishmania Tarentolae Mitochondrial Large Ribosomal Subunit Model Deposited 2009-04-20 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 19 PDB declaration: eicosameric
Chain S 11–126（116 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer 50 mM Tris HCL, pH 7.5, 100mM KCL, 10mM MgCl2, 3mM DTT, 0.1mM EDTA, 0.05% dodecyl maltoside；pH 7.5；50 mM Tris HCL, pH 7.5, 100mM KCL, 10mM MgCl2, 3mM DTT, 0.1mM EDTA, 0.05% dodecyl maltoside
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 14.10 Å
3J7Y Structure of the large ribosomal subunit from human mitochondria Deposited 2014-08-26 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain O 1–175（175 aa）
Not recorded AMP ADENOSINE MONOPHOSPHATE × 1 MG MAGNESIUM ION × 66 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer 20 mM HEPES-KOH, pH 7.45, 100 mM potassium chloride, 20 mM magnesium acetate, 2 mM DTT；pH 7.45；20 mM HEPES-KOH, pH 7.45, 100 mM potassium chloride, 20 mM magnesium acetate, 2 mM DTT
cryo-EM vitrification conditions 90 K；Cryogen ETHANE；Blot 2.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK II).
Resolution 3.40 Å
3J9M Structure of the human mitochondrial ribosome (class 1) Deposited 2015-02-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 85-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 127 ZN ZINC ION × 7 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer 20 mM HEPES-KOH, pH 7.45, 100 mM KCl, 20 mM MgOAc, 2 mM DTT；pH 7.45；20 mM HEPES-KOH, pH 7.45, 100 mM KCl, 20 mM MgOAc, 2 mM DTT
cryo-EM vitrification conditions Blot 2.5 seconds before plunging；90 K；Cryogen ETHANE；Blot 2.5 seconds before plunging into liquid ethane (FEI VITROBOT MARK II).
Resolution 3.50 Å
5OOL Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA Deposited 2017-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 92 ZN ZINC ION × 3 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.45；2 mM Synercid (Santa Cruz Biotechnology, Inc) was added to reduce preferential orientation.
cryo-EM vitrification conditions Cryogen ETHANE；Sample incubated for 30 s prior to freezing.
Resolution 3.06 Å
5OOM Structure of a native assembly intermediate of the human mitochondrial ribosome with unfolded interfacial rRNA Deposited 2017-08-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 55-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 49 ZN ZINC ION × 2 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.45；2 mM Synercid (Santa Cruz Biotechnology, Inc) was added to reduce preferential orientation.
cryo-EM vitrification conditions Cryogen ETHANE；Sample incubated for 30 s prior to freezing.
Resolution 3.03 Å
6I9R Large subunit of the human mitochondrial ribosome in complex with Virginiamycin M and Quinupristin Deposited 2018-11-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 53-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 134 H8T Virginiamycin M × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6NU2 Structural insights into unique features of the human mitochondrial ribosome recycling Deposited 2019-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 82 PDB declaration: 86-meric
Chain O 9–160（152 aa）
Not recorded MG MAGNESIUM ION × 127 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.90 Å
6NU3 Structural insights into unique features of the human mitochondrial ribosome recycling Deposited 2019-01-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 85-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 127 ZN ZINC ION × 7 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
6VLZ Structure of the human mitochondrial ribosome-EF-G1 complex (ClassI) Deposited 2020-01-27 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 85 PDB declaration: 90-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 130 ZN ZINC ION × 7 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.97 Å
6VMI Structure of the human mitochondrial ribosome-EF-G1 complex (ClassIII) Deposited 2020-01-28 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 85 PDB declaration: 91-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 130 ZN ZINC ION × 7 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.96 Å
6ZM5 Human mitochondrial ribosome in complex with OXA1L, mRNA, A/A tRNA, P/P tRNA and nascent polypeptide Deposited 2020-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 88 PDB declaration: 94-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 189 K POTASSIUM ION × 44 ZN ZINC ION × 3 FES FE2/S2 (INORGANIC) CLUSTER × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ALA ALANINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
6ZM6 Human mitochondrial ribosome in complex with mRNA, A/A tRNA and P/P tRNA Deposited 2020-07-01 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 86 PDB declaration: 92-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 189 K POTASSIUM ION × 44 ZN ZINC ION × 3 FES FE2/S2 (INORGANIC) CLUSTER × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.59 Å
6ZS9 Human mitochondrial ribosome in complex with ribosome recycling factor Deposited 2020-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 88 PDB declaration: 91-meric
Chain XO 1–175（175 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 195 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6ZSA Human mitochondrial ribosome bound to mRNA, A-site tRNA and P-site tRNA Deposited 2020-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 86 PDB declaration: 92-meric
Chain XO 1–175（175 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 195 H8Q ~{N}-[(3~{S},6~{R},12~{R},15~{S},16~{S},19~{S},22~{S},25~{S})-25-[[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]sulfanylmethyl]-3-[[4-(dimethylamino)phenyl]methyl]-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptakis(oxidanylidene)-19-phenyl-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-pyridine-2-carboxamide × 1 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
6ZSB Human mitochondrial ribosome in complex with mRNA and P-site tRNA Deposited 2020-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 87 PDB declaration: 92-meric
Chain XO 1–175（175 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 195 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.50 Å
6ZSC Human mitochondrial ribosome in complex with E-site tRNA Deposited 2020-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 87 PDB declaration: 91-meric
Chain XO 1–175（175 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 195 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
6ZSD Human mitochondrial ribosome in complex with mRNA, P-site tRNA and E-site tRNA Deposited 2020-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 87 PDB declaration: 93-meric
Chain XO 1–175（175 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 195 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
6ZSE Human mitochondrial ribosome in complex with mRNA, A/P-tRNA and P/E-tRNA Deposited 2020-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 87 PDB declaration: 93-meric
Chain XO 1–175（175 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 195 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.00 Å
6ZSG Human mitochondrial ribosome in complex with mRNA, A-site tRNA, P-site tRNA and E-site tRNA Deposited 2020-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 87 PDB declaration: 94-meric
Chain XO 1–175（175 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 195 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.00 Å
7A5F Structure of the stalled human mitoribosome with P- and E-site mt-tRNAs Deposited 2020-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 85 PDB declaration: 91-meric
Chain O3 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 128 ZN ZINC ION × 7 GDP GUANOSINE-5'-DIPHOSPHATE × 1 SO4 SULFATE ION × 1 MLI MALONATE ION × 3 CL CHLORIDE ION × 2 NA SODIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.40 Å
7A5G Structure of the elongating human mitoribosome bound to mtEF-Tu.GMPPCP and A/T mt-tRNA Deposited 2020-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 86 PDB declaration: 94-meric
Chain O3 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 128 SPD SPERMIDINE × 1 ZN ZINC ION × 7 GDP GUANOSINE-5'-DIPHOSPHATE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 NA SODIUM ION × 4 SO4 SULFATE ION × 1 MLI MALONATE ION × 3 CL CHLORIDE ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 4.33 Å
7A5H Structure of the split human mitoribosomal large subunit with rescue factors mtRF-R and MTRES1 Deposited 2020-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 59-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 92 ZN ZINC ION × 2 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7A5I Structure of the human mitoribosome with A- P-and E-site mt-tRNAs Deposited 2020-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 83 PDB declaration: 90-meric
Chain O3 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 127 ZN ZINC ION × 7 CL CHLORIDE ION × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7A5J Structure of the split human mitoribosomal large subunit with P-and E-site mt-tRNAs Deposited 2020-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 59 PDB declaration: 63-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 92 ZN ZINC ION × 3 CL CHLORIDE ION × 2 NA SODIUM ION × 4 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7A5K Structure of the human mitoribosome in the post translocation state bound to mtEF-G1 Deposited 2020-08-21 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 86 PDB declaration: 93-meric
Chain O3 1–175（175 aa）
Not recorded GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 MG MAGNESIUM ION × 128 SPD SPERMIDINE × 1 ZN ZINC ION × 7 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7L08 Cryo-EM structure of the human 55S mitoribosome-RRFmt complex. Deposited 2020-12-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 87-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 127 ZN ZINC ION × 7 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.49 Å
7L20 Cryo-EM structure of the human 39S mitoribosomal subunit in complex with RRFmt and EF-G2mt. Deposited 2020-12-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 57-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 102 ZN ZINC ION × 3 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.15 Å
7O9K Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1, the MALSU module, GTPBP5 and mtEF-Tu Deposited 2021-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 67 PDB declaration: 69-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 93 SAM S-ADENOSYLMETHIONINE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 SAH S-ADENOSYL-L-HOMOCYSTEINE × 1 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7O9M Human mitochondrial ribosome large subunit assembly intermediate with MTERF4-NSUN4, MRM2, MTG1 and the MALSU module Deposited 2021-04-16 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 66-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 104 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ZN ZINC ION × 2 SAM S-ADENOSYLMETHIONINE × 1 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7ODR State A of the human mitoribosomal large subunit assembly intermediate Deposited 2021-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 57-meric
Chain O 1–175（175 aa）
Not recorded PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 97 K POTASSIUM ION × 2 FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；4 uL of the sample was blotted for 2-6 sec before plunging
Resolution 2.90 Å
7ODS State B of the human mitoribosomal large subunit assembly intermediate Deposited 2021-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain O 1–175（175 aa）
Not recorded PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 MG MAGNESIUM ION × 88 K POTASSIUM ION × 8 N ANY 5'-MONOPHOSPHATE NUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；4 uL of the sample was blotted for 2-6 sec before plunging
Resolution 3.10 Å
7ODT State C of the human mitoribosomal large subunit assembly intermediate Deposited 2021-04-30 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain O 1–175（175 aa）
Not recorded GDP GUANOSINE-5'-DIPHOSPHATE × 1 MG MAGNESIUM ION × 95 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 ZN ZINC ION × 2 K POTASSIUM ION × 10 FES FE2/S2 (INORGANIC) CLUSTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE；4 uL of the sample was blotted for 2-6 sec before plunging
Resolution 3.10 Å
7OF0 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset1). Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 61 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.20 Å
7OF2 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with GTPBP6. Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 85 GTP GUANOSINE-5'-TRIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7OF3 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 (dataset2). Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 58 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7OF4 Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6 (PTC conformation 1). Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 53-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 89 GTP GUANOSINE-5'-TRIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.70 Å
7OF5 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset2). Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 57-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 70 GTP GUANOSINE-5'-TRIPHOSPHATE × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
7OF6 Structure of mature human mitochondrial ribosome large subunit in complex with GTPBP6 (PTC conformation 2). Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 51 PDB declaration: 53-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 88 GTP GUANOSINE-5'-TRIPHOSPHATE × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.60 Å
7OF7 Structure of a human mitochondrial ribosome large subunit assembly intermediate in complex with MTERF4-NSUN4 and GTPBP5 (dataset1). Deposited 2021-05-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 57-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 74 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.50 Å
7OG4 Human mitochondrial ribosome in complex with P/E-tRNA Deposited 2021-05-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 86 PDB declaration: 90-meric
Chain XO 1–175（175 aa）
Not recorded ZN ZINC ION × 7 MG MAGNESIUM ION × 195 H8Q ~{N}-[(3~{S},6~{R},12~{R},15~{S},16~{S},19~{S},22~{S},25~{S})-25-[[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]sulfanylmethyl]-3-[[4-(dimethylamino)phenyl]methyl]-12-ethyl-4,16-dimethyl-2,5,11,14,18,21,24-heptakis(oxidanylidene)-19-phenyl-17-oxa-1,4,10,13,20-pentazatricyclo[20.4.0.0^{6,10}]hexacosan-15-yl]-3-oxidanyl-pyridine-2-carboxamide × 1 DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.80 Å
7OI6 Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 1 Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 52-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 48 ZN ZINC ION × 1 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 5.70 Å
7OI7 Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 2 Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 49 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OI8 Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 3A Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 55-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 49 ZN ZINC ION × 2 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7OI9 Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 3B Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 52 PDB declaration: 54-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 49 ZN ZINC ION × 2 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OIA Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 3C Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 52-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 49 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
7OIB Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 3D Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 49 PDB declaration: 51-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 49 ZN ZINC ION × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
7OIC Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 4 Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 55 PDB declaration: 58-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 76 ZN ZINC ION × 3 PNS 4'-PHOSPHOPANTETHEINE × 1 SAM S-ADENOSYLMETHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
7OID Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 5A Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 56-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.70 Å
7OIE Cryo-EM structure of late human 39S mitoribosome assembly intermediates, state 5B Deposited 2021-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 55-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 2 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.50 Å
7PD3 Structure of the human mitoribosomal large subunit in complex with NSUN4.MTERF4.GTPBP7 and MALSU1.L0R8F8.mt-ACP Deposited 2021-08-04 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 60-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 91 PNS 4'-PHOSPHOPANTETHEINE × 1 SAM S-ADENOSYLMETHIONINE × 1 GCP PHOSPHOMETHYLPHOSPHONIC ACID GUANYLATE ESTER × 2 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
7PO4 Assembly intermediate of human mitochondrial ribosome large subunit (largely unfolded rRNA with MALSU1, L0R8F8 and ACP) Deposited 2021-09-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 60-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 35 K POTASSIUM ION × 8 ZN ZINC ION × 1 FES FE2/S2 (INORGANIC) CLUSTER × 1 8Q1 S-[2-({N-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alanyl}amino)ethyl] dodecanethioate × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.56 Å
7QH6 Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 1 Deposited 2021-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 44 PDB declaration: 46-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
7QH7 Cryo-EM structure of the human mtLSU assembly intermediate upon MRM2 depletion - class 4 Deposited 2021-12-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 47 PDB declaration: 49-meric
Chain O 9–160（152 aa）
Not recorded MG MAGNESIUM ION × 50 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.89 Å
7QI4 Human mitochondrial ribosome at 2.2 A resolution (bound to partly built tRNAs and mRNA) Deposited 2021-12-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 87 PDB declaration: 94-meric
Chain O 1–175（175 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 1 SPD SPERMIDINE × 4 MG MAGNESIUM ION × 206 K POTASSIUM ION × 54 ZN ZINC ION × 3 FES FE2/S2 (INORGANIC) CLUSTER × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PUT 1,4-DIAMINOBUTANE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.21 Å
7QI5 Human mitochondrial ribosome in complex with mRNA, A/A-, P/P- and E/E-tRNAs at 2.63 A resolution Deposited 2021-12-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 87 PDB declaration: 94-meric
Chain O 1–175（175 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 1 SPD SPERMIDINE × 4 MG MAGNESIUM ION × 208 K POTASSIUM ION × 54 ZN ZINC ION × 3 FES FE2/S2 (INORGANIC) CLUSTER × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PUT 1,4-DIAMINOBUTANE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.63 Å
7QI6 Human mitochondrial ribosome in complex with mRNA, A/P- and P/E-tRNAs at 2.98 A resolution Deposited 2021-12-14 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 87 PDB declaration: 93-meric
Chain O 1–175（175 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 1 SPD SPERMIDINE × 4 K POTASSIUM ION × 54 MG MAGNESIUM ION × 202 ZN ZINC ION × 3 FES FE2/S2 (INORGANIC) CLUSTER × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PUT 1,4-DIAMINOBUTANE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
8ANY Human mitochondrial ribosome in complex with LRPPRC, SLIRP, A-site, P-site, E-site tRNAs and mRNA Deposited 2022-08-06 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 89 PDB declaration: 96-meric
Chain O 1–175（175 aa）
Not recorded NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 1 SPD SPERMIDINE × 4 MG MAGNESIUM ION × 206 K POTASSIUM ION × 49 ZN ZINC ION × 3 FES FE2/S2 (INORGANIC) CLUSTER × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 PUT 1,4-DIAMINOBUTANE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.85 Å
8K2A Cryo-EM structure of the human 55S mitoribosome with Tigecycline Deposited 2023-07-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 83-meric
Chain LQ 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 145 T1C TIGECYCLINE × 4 ZN ZINC ION × 7 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
8K2B Cryo-EM structure of the human 39S mitoribosome with Tigecycline Deposited 2023-07-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 55-meric
Chain LQ 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 95 T1C TIGECYCLINE × 1 ZN ZINC ION × 3 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.40 Å
8OIR 55S human mitochondrial ribosome with mtRF1 and P-site tRNA Deposited 2023-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 88 PDB declaration: 94-meric
Chain BV 1–175（175 aa）
Not recorded K POTASSIUM ION × 51 MG MAGNESIUM ION × 354 VAL VALINE × 1 ZN ZINC ION × 3 FS2 FE-S-O HYBRID CLUSTER × 3 MET METHIONINE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 3.10 Å
8OIT 39S human mitochondrial large ribosomal subunit with mtRF1 and P-site tRNA Deposited 2023-03-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 58 PDB declaration: 62-meric
Chain BV 1–175（175 aa）
Not recorded K POTASSIUM ION × 34 MG MAGNESIUM ION × 228 VAL VALINE × 1 ZN ZINC ION × 2 FS2 FE-S-O HYBRID CLUSTER × 1 MET METHIONINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE-PROPANE
Resolution 2.90 Å
8PK0 human mitoribosomal large subunit assembly intermediate 1 with GTPBP10-GTPBP7 Deposited 2023-06-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 1 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 96 K POTASSIUM ION × 10 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.03 Å
8QSJ Human mitoribosomal large subunit assembly intermediate 2 with GTPBP7 Deposited 2023-10-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 56 PDB declaration: 58-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 38 FES FE2/S2 (INORGANIC) CLUSTER × 1 PM8 S-(2-{[N-(2-HYDROXY-4-{[HYDROXY(OXIDO)PHOSPHINO]OXY}-3,3-DIMETHYLBUTANOYL)-BETA-ALANYL]AMINO}ETHYL) DECANETHIOATE × 1 SAM S-ADENOSYLMETHIONINE × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.6
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å
8QU1 mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 1 Deposited 2023-10-13 Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–175（175 aa）
Not recorded No recorded non-water small molecule ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.74 Å
8QU5 mt-LSU assembly intermediate in GTPBP8 knock-out cells, state 2 Deposited 2023-10-13 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 53 PDB declaration: 55-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 2 MG MAGNESIUM ION × 48 PNS 4'-PHOSPHOPANTETHEINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.42 Å
8RRI Human mitochondrial ribosome in complex with antibiotic tigecycline Deposited 2024-01-22 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 86-meric
Chain O 1–175（175 aa）
Not recorded VAL VALINE × 1 MG MAGNESIUM ION × 94 FES FE2/S2 (INORGANIC) CLUSTER × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 T1C TIGECYCLINE × 3 K POTASSIUM ION × 16 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.40 Å
8XT0 Cryo-EM structure of the human 55S mitoribosome with 5um Tigecycline Deposited 2024-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 83-meric
Chain LQ 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 145 T1C TIGECYCLINE × 3 ZN ZINC ION × 7 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.20 Å
8XT1 Cryo-EM structure of the human 39S mitoribosome with 5uM Tigecycline Deposited 2024-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 52-meric
Chain LQ 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 95 T1C TIGECYCLINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
8XT2 Cryo-EM structure of the human 55S mitoribosome with 10uM Tigecycline Deposited 2024-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 80 PDB declaration: 83-meric
Chain LQ 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 145 T1C TIGECYCLINE × 3 ZN ZINC ION × 7 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.30 Å
8XT3 Cryo-EM structure of the human 39S mitoribosome with 10uM Tigecycline Deposited 2024-01-10 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 50 PDB declaration: 52-meric
Chain LQ 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 95 T1C TIGECYCLINE × 1 ZN ZINC ION × 3 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.10 Å
9CN3 Human 39S mitoribosome in complex with antibiotic Linezolid Deposited 2024-07-15 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 54 PDB declaration: 56-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 MG MAGNESIUM ION × 102 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.62 Å
9OLF Membrane-associated human mitoribosome in complex with TACO1 Deposited 2025-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 93 PDB declaration: 100-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 SPD SPERMIDINE × 7 MG MAGNESIUM ION × 205 PUT 1,4-DIAMINOBUTANE × 1 K POTASSIUM ION × 54 SPM SPERMINE × 2 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 3 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.46 Å
9PG8 In situ structure of the human mitoribosome in the P-E state Deposited 2025-07-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 86 PDB declaration: 93-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 8 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 205 VAL VALINE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.06 Å
9PGF In situ structure of the human mitoribosome in the P state Deposited 2025-07-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 86 PDB declaration: 91-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 8 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 205 VAL VALINE × 1 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.93 Å
9PGI In situ structure of the human mitoribosome in the A-P-E state with TACO1 Deposited 2025-07-07 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 87 PDB declaration: 94-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 7 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 204 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.02 Å
9PGL In situ structure of the human mitoribosome in the A-P state with TACO1 Deposited 2025-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 86 PDB declaration: 92-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 8 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 204 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.90 Å
9PGM In situ structure of the human mitoribosome in the P-E state from TACO1-knockout cells Deposited 2025-07-08 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 85 PDB declaration: 91-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 7 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 204 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.18 Å
9PR4 In Situ Structure of the Human Mitochondrial Large Subunit 39S in Complex with TACO1 Deposited 2025-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 61 PDB declaration: 63-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 2 K POTASSIUM ION × 36 MG MAGNESIUM ION × 141 FES FE2/S2 (INORGANIC) CLUSTER × 1 SPD SPERMIDINE × 2 PUT 1,4-DIAMINOBUTANE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.77 Å
9PRA In Situ Structure of the Human Mitoribosome Large Subunit 39S in Complex with EF-Tu Deposited 2025-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 64 PDB declaration: 66-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 2 K POTASSIUM ION × 36 MG MAGNESIUM ION × 141 FES FE2/S2 (INORGANIC) CLUSTER × 1 SPD SPERMIDINE × 2 PUT 1,4-DIAMINOBUTANE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.83 Å
9PRD In situ structure of the human mitoribosome in the P state from TACO1-knockout cells Deposited 2025-07-23 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 89-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 7 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 204 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.31 Å
9PRQ In situ structure of human mitoribosome in the A/T-P state from TACO1-knockout cells Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 85 PDB declaration: 91-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 7 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 204 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.34 Å
9PRX In situ structure of the human mitoribosome in the A-P state from TACO1-knockout cells Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 84 PDB declaration: 90-meric
Chain O 1–175（175 aa）
Not recorded VAL VALINE × 1 ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 7 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 204 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.23 Å
9PS0 In situ structure of the human mitoribosome in the A/P-P/E state from TACO1-knockout cells Deposited 2025-07-24 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 85 PDB declaration: 91-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 52 SPD SPERMIDINE × 7 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 204 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 2 FES FE2/S2 (INORGANIC) CLUSTER × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.29 Å
9PS7 In situ structure of the human mitoribosome in the A/T-P-E state from TACO1-knockout cells Deposited 2025-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 86 PDB declaration: 93-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 7 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 204 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.08 Å
9PSI In situ structure of the human mitoribosome in the A-P-E state from TACO1-knockout cells Deposited 2025-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 85 PDB declaration: 92-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 7 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 204 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.12 Å
9PSM In situ structure of the human mitoribosome in the A/P-P/E state Deposited 2025-07-25 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 87 PDB declaration: 93-meric
Chain O 1–175（175 aa）
Not recorded ZN ZINC ION × 3 K POTASSIUM ION × 54 SPD SPERMIDINE × 8 PUT 1,4-DIAMINOBUTANE × 1 MG MAGNESIUM ION × 204 FES FE2/S2 (INORGANIC) CLUSTER × 3 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPM SPERMINE × 2 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 VAL VALINE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.4
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 2.98 Å
9UWH human mitoribosome trapped by retapamulin Deposited 2025-05-12 Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 81 PDB declaration: 86-meric
Chain O 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 208 K POTASSIUM ION × 53 G34 Retapamulin × 1 VAL VALINE × 1 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 1 SPD SPERMIDINE × 1 ZN ZINC ION × 3 FES FE2/S2 (INORGANIC) CLUSTER × 3 ATP ADENOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 ELECTRON MICROSCOPY
cryo-EM buffer pH 7.5
cryo-EM vitrification conditions Cryogen ETHANE
Resolution 3.00 Å

87 other PDB entries and 87 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q9NRX2_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 8–116； UniProt 28–136

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 2cqm

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2cqm
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2cqm
Deposition date deposition_date2005-05-20
Structure title titleSolution structure of the mitochondrial ribosomal protein L17 isolog
Keywords keywords;alpha and beta (a+b), Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Translation ;; TRANSLATION
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.25 Å
Radius of gyration Rg (electron density) rg_electron15.76 Å
Forward intensity I(0) i01047300000.00
Molecular weight molecular_weight273040.0 kDa
Excluded volume excluded_volume341960 ų
Envelope volume envelope_volume46732 ų
Hydration-shell volume shell_volume19674 ų
Envelope diameter envelope_diameter70.8 Å
Shell Rg shell_rg26.63 Å
Envelope Rg envelope_rg21.21 Å
Shape Rg shape_rg15.74 Å
Total Rg total_rg16.03 Å
Total atoms total_atoms38620
Residues n_residues2440
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax65.2 Å
Rg (real space) rg_real16.35 Å
Rg uncertainty (real space) rg_real_error0.68 Å
I(0) (real space) i0_real1.0470e+09
I(0) uncertainty (real space) i0_real_error1.3670e+07
Rg (reciprocal space) rg_reciprocal16.34 Å
I(0) (reciprocal space) i0_reciprocal1047000000.0000
Solution quality estimate total_estimate0.7495
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary63.5 Å
Skewness Skewness skewness0.575
Kurtosis Kurtosis kurtosis0.233
Angular range angular_range— – 0.4900 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha622900.0000
Real-space data points n_real_points79
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.355; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.676; Smooth: 0.999
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2cqma1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.188 — Prokaryotic ribosomal protein L17
Superfamily Superfamily superfamilyd.188.1 — Prokaryotic ribosomal protein L17
Family Family familyd.188.1.1 — Prokaryotic ribosomal protein L17
Domain ID domain_idd2cqma2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2cqma3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2cqmA01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1030 — 50s Ribosomal Protein L17; Chain: A,
Homologous superfamily homologous superfamily10 — Ribosomal protein L17
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8. Citations (1)

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9. Files and Curves (10)